Introduction to dataset

  • Nature article: Microbial composition on the International Space Station
  • Article plots them in stacked barplots
  • Two datasets: no. reads per sample, sorted by Taxonomic classification (Domain, Phylum, Genus)
  • Sorted into sampling session (A,B,C)

SD1

  • Supplementary data 1 (fig 1): RSV table (ribosomal sequence variants - OTU alternative)
    Taxonomic classification
    k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;gFaecalibacterium;s
    k__Bacteria;p__Cyanobacteria;c__Melaibacteria;oGastraerophilales;f;g;s
    k__Bacteria;p__Planctomycetes;c__Phycisphaerae;oWD2101_soil_group;f;g;s
    k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomodales;f__Moraxellaceae;gMoraxella;s
    k__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Actinomycetales;f__Actinomycetaceae;gActinomyces;s
    k__Bacteria;p__Proteobacteria;c__Betaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;gLautropia;s

SD2

  • Supplementary data 2 (fig 4): Taxonomic diversity inferred from metagenomic dataset
    domain phylum className order family genus COLA1 COLB1 N2A N2B N3C1 N1C
    Viruses unclassified (derived from Viruses) unclassified (derived from Viruses) Caudovirales Podoviridae AHJD-like viruses 11 130 2 25 32 33
    Bacteria Firmicutes Bacilli Lactobacillales Aerococcaceae Abiotrophia 17 898 10 98 102 119
    Eukaryota unclassified (derived from Eukaryota) unclassified (derived from Eukaryota) unclassified (derived from Eukaryota) unclassified (derived from Eukaryota) Acanthamoeba 0 1 0 0 0 0
    Bacteria Cyanobacteria unclassified (derived from Cyanobacteria) unclassified (derived from Cyanobacteria) unclassified (derived from Cyanobacteria) Acaryochloris 8 22 10 11 12 3
    Bacteria Firmicutes Clostridia Clostridiales Ruminococcaceae Acetivibrio 5 35 1 40 17 5
    Bacteria Proteobacteria Alphaproteobacteria Rhodospirillales Acetobacteraceae Acetobacter 7 14 17 9 19 10

    • Table 1

  • Table 1 (tidy): sampling locations and sampling sessions
    Sampled_surface ISS_module Wipe Session
    Ambient air (field blank, FB) Columbus A5 A
    Ambient air (field blank, FB) Columbus A5 B
    Ambient air (field blank, FB) Columbus B1 A
    Ambient air (field blank, FB) Columbus B1 B
    Light covers Columbus A4 A
    Light covers Columbus A4 B
    Light covers Columbus B2 A
    Light covers Columbus B2 B
    SCC laptop Columbus A2 A
    SCC laptop Columbus A2 B

    • Data Processing Workflow

    Results & Discussion

    Figure 1: Domain

    Figure 1: Phylum

    Figure 1: Genus

    Figure 1 discussion

    • Phylum: they have an ‘unknown’ section, but we can’t find that in the data
    • Genus: They haven’t normalised, they haven’t provided clean room data, they have multiple sections in barograph not shown in legend, their colour choice is bad: unknown and lactobacillus are very difficult to distinguish

    Figure 4: Domain

    Figure 4: Phylum

    Figure 4: Genus

    Figure 4 Discussion

    • General: Their use of sqrt(TSS) makes no sense
    • Method of selection unclear; solution: sorted top 100
    • Domain: ‘other sequences’ not visible in out plot, but there is only 1 read
      domain n
      Archaea 59
      Bacteria 592
      Eukaryota 390
      other sequences 1
      Viruses 73
    • Genus: we filtered out all non-bacteria